As virtually everyone knows, Apple has had a sweet run of late. This year alone its stock shot up nearly 50%, four times the gains notched by the S&P 500 index.

But if you’re feeling miffed that you missed out on the stock of the decade, well, maybe you didn’t miss out after all. Many Apple investors have even started to worry that they may actually own too much.

Why is that? Because many investors rely on mutual funds or exchange-traded funds that mimic the S&P 500 to build a diversified portfolio. And as I noted recently, Apple accounts for about 11% of the gains in the broad index. Without Apple, the index would still be below 1,400, an important psychological benchmark. “A lot of investors don’t know what’s in their portfolios,” Howard Silverblatt, senior index analyst at S&P Indices. “It’s not as easy as it used to be.”

Silverblatt discovered that a lot of people — both pros and individual investors — didn’t understand just how powerful the Apple effect was on their returns. Last month he sent an e-mail blast with a great piece of news: the information-technology sector of the S&P was nearly 10% higher than the October 2007 market high. Did anyone know what the performance of the S&P tech sector would look like without Apple in the mix? The answer: down more than 4%.

The phone began ringing. Really? Is the Apple effect that big? Yes, indeed, it is. And it is even more pronounced for people who own high-tech funds.

This isn’t only an Apple phenomenon, of course. Silverblatt notes a lot of people have too much invested in other stocks without realizing it. A fan of the energy sector might decide to invest in something that mimics the S&P energy sector. But over time, that investor could wind up far from diversified. Exxon accounts for 28% of the performance. “That’s not good or bad. You just need to know it,” Silverblatt says.

Apple drew Silverblatt’s notice because it is now the world’s biggest company and it’s growing at a phenomenal pace. He remembers when IBM dominated the S&P even more decisively than Apple does today. From 1981 to ’83 Big Blue surged 134%, eventually accounting for 6.3% of the S&P index (vs. 4.4% for Apple today). IBM had a nice run — but it didn’t last forever. Upstarts with new ideas overtook the computing giant. Apple may be no less vulnerable. Says Silverblatt: “What helps you on the way up kills on the way down.”

Even professional investors can get blindsided by this phenomenon, says Bob Doll, chief equity strategist for fundamental equities at BlackRock asset management. He also notes that while portfolio managers often try to explain away a bad quarter by saying, Look, only three stocks were responsible for their lousy returns, they never go out of their way to tell investors that three stocks saved their necks.

Apple has been unbelievably sweet. But do you know just how big a bite you’ve taken?